3IY8 Ribosome date Apr 16, 2009
title Leishmania Tarentolae Mitonchondrial Ribosome Small Subunit
authors M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, R.K.Agrawal
compound source
Molecule: Leishmania Tarentolae Mitochondrial Small Subunit
Chain: A
 Organism_scientific: Leishmania Tarentolae
Organism_taxid: 5689

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S6
Chain: F
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Escherichia Coli
Organism_taxid: 83333

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 14.10 Å
Gene
Ontology
ChainFunctionProcessComponent
E


F


H


I


K


L


O


P


Q


R


Primary referenceStructure of a mitochondrial ribosome with minimal RNA., Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK, Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9637-42. Epub 2009 Jun 3. PMID:19497863
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (3iy8.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 3IY8
  • Likely Quarternary Molecular Structure file(s) for 3IY8
  • Retrieve 3IY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IY8 from S2C, [Save to disk]
    • View 3IY8 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3IY8
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3IY8, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iy8] [3iy8_L] [3iy8_E] [3iy8_O] [3iy8_R] [3iy8_K] [3iy8_I] [3iy8_P] [3iy8_A] [3iy8_F] [3iy8_H] [3iy8_Q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3IY8: [Ribosomal_S15 ] by SMART
    • Other resources with information on 3IY8
  • Community annotation for 3IY8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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